Will Marvel comic book characters make any appearances in the S.H.I.E.L.D. TV series?

Unknown, but Clark Gregg from the Avengers and Iron Man 2 will reprise his role as Agent Coulson.

Deadline.com reported in August 2012 that S.H.I.E.L.D. got
the green light:

"S.H.I.E.L.D. will be written by Whedon and frequent collaborators, his brother Jed Whedon and Maurissa Tancharoen. Joss Whedon also is set to direct the pilot, schedule permitting. Production on the pilot, which marks the first live-action Marvel TV project to get a green light, will start immediately. Joss Whedon, Jed Whedon, and Tancharoen executive produce with Jeffrey Bell and Marvel TV's Jeph Loeb."

ABC President Paul Lee said this about S.H.I.E.L.D. in an IGN interview:

"There is no question that it is part of the Marvel Universe. In fact, the story takes place after the battle for New York. This is S.H.I.E.L.D. They're following their own particular stories. There are characters in it, Coulson, who clearly comes from the Avengers. So it's part of the world, but we're going to be very, very careful that we don't tread on the toes of the features and build a whole new world. And that's what Joss Whedon does better than anybody else. He's built a world for us."
Fans should be very excited about this new Joss Whedon TV series.